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RiceLncPedia: a curated knowledgebase of rice Long non-coding RNAs
Sequence

>Osa09LNT0434500.1

TCCAGTGCATGCAAATATAGATGACCAAAGTATGGAACTTCCAGTTCACAAGTTCCAGTGCATGCCAACATATATGACCAAAAGAACCGAACTTCCAGTTCACAAGTTCCAGCGCATGCCAACATGGCAACATATATGACCAAAAGGCAACAGGCAGCCAACCTAAGGCAACAGACACAGCGAACATCTACTAGAGTTCCATGTGGCCTAAAGTTCAGGTAAACCTACATAATTAACAAAAGACTACTTAGTGAGACAACCACAACCAACAGCTATCCAAGTTCATGGCCATGACCATCCAGGTCAGTTTAGTTACAAAATATATCCATAGTTTTAGGAATGTACAACTAGTCCGCTGTCATGCTAAAAGTTGACAATTGCACCAGATGCAGCACCAACCCCAACATGGTTGGGGCCTGAGTTTCCATTCGAAGCCACAGGTCCAGACGAAGCTAGGTGAGTCAACATGACAGGTAAGGGAGGTGTGCCTGAAGCTGACAAGTCTATGTTCAGCTTACTTTGTATCACCCTTAAAGCAGCTTCAAAGAATGCTGATTTCTGTTGAGAGGCTATCTTTTCCAACTCCCTCTCCTTGCGCTCTTCCTCCCTCTCCTTACGCTCCTGCTCCTTCTCTCGCGCCCTCTCTTCACGCTCACACTCCTTCTCCTGCTCCTTCTCCTGCCGCTCCCTCTCCTTCTCACGCTCCCTCTCTTCACGCTCTCGCTCCCTTGCCTCGCGCTCCTCTTGTAGTTGCCGCAGAAGGTCTTCAACCTGGTTTGTGTTGTCATGATCTGTCCTCAATCTTCTGCGAGGGCGTTGATCATCACGCGAATTATCACCAAACACTGCTGATGAGTCAATGAGTCCATCACCAATCATGAAACGGCCATGTTTCTTTCCACCACCAGCCATGTGCACAGCGACAGGATCAATGGGAGAAGTGCGCCAATCATTTTCTGGCCCATGCAACTGAACATAAGCTGCAGCATAGGCCTCAAGCTTCTCAGCTACACGCGGGTCACAGCTGAATTGTCCATCCTCTCGATTTTCCCTCCTTCCTTCTGTGTAGGCCTCTAGTGGAGCAACTGGCCGCTTTTTCTTCTTCTCCAAATTTTTTTGGTAACGGCTCAAGTTAGCACTGCCTTGGCGGTGAGATGGCCCTTTCATTTTCTCCCTCCGTATCCTATGAGCACGTGAGACAGCCTGCCATTTTGGATTACACCACCGCAATCGTATCAACTCCCGCCATGCATTTTCTGAATTCAGGAACCACCATGGTTCTACCTTTAGGTACTCGCTCTCTGTAAGATAAGTTCTGCATGCGATTTCTCTGGAAGTGTTCACCTTCAGGATTTTCCTTTGGTAATTAAGCACAGCTAGGATGCGAGTTTCATAAAACAAGCGATCAACAAGGCCCTTGACACAATTGTGGACAACCTTTCTAGCTTCTTGTTCTTTTCCCTCTGCCCACCTGAAGTAAAGCCAGAAGTCTTCCTCAACACGATGGAGACAGCTTGGCAGCCGTATTTGATTGCTTCTTGGAGTATCCGGCGCTATCCTGTAATGTTTCCAACTCCATGCTGGCTCCTCTTTACCCTTCAATGTGACAATGCCAGGGAACCATTGTTTAAGAAGTAATGTCAGGATGCTATTGGGGACCCTAATGTTGCCTCCATAATCATTTGCTCGCCATTGCCTGTCTCCTACTGGAGTCAGCACAGGTTTGTCCTCCTCTCGGGTAGGTTGTGGTGGCACACGTGTAGGACCACGAAACCAGATTTCCTCAGATGTTTCTTCCTCCTCCAAAATCTCCTCATCCAAATTAGGAGAATGATTAGGTTGTTGGGAACATGAGGACCTTGTACTGCATCTGGGCAAGGTAGCACCACTCACTGCCTGATCTGAACAATTGGAAGCCTCCCTATTGCCTAAGCTCAAGCGCCGCATATTCCTCACCCTGCTCAGTTGCTTCTTGATCGGGGACTGGGGAGCCTTGCTGCACAGCTTGACGAGGATGTACTGGTCAGCGCAGTGGATGCCTGGATGGACGTGGACGTACAGGGCCTCGTAGATGGAGTGGGATGCGACCCCTCGTCGACCGGGGACGCGCTGCCACCCTCGCCGGCCTAGCCGGGGACGCACGGCCGGCCGTGAACGGAGAGACCGAGAGGGGAGAAGTGAAGCGGCGGGGGTGGGGATGGG

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.994466
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa09LNT0434500.1 9 10980397 G A
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa09LNT0434500.1 osa-miR812t Translation 5.0 15.564 1 24
Osa09LNT0434500.1 osa-miR812u Translation 5.0 15.564 1 24
Osa09LNT0434500.1 osa-miR1437b-5p Translation 4.5 15.796 1 21
Osa09LNT0434500.1 osa-miR159a.2 Translation 4.0 18.903 1 21
Osa09LNT0434500.1 osa-miR1423-5p Cleavage 4.5 16.917 1 24
Osa09LNT0434500.1 osa-miR444b.1 Translation 4.5 19.183 1 21
Osa09LNT0434500.1 osa-miR444c.1 Translation 4.5 19.183 1 21
Osa09LNT0434500.1 osa-miR2092-5p Cleavage 5.0 15.291 1 21
Osa09LNT0434500.1 osa-miR2104 Cleavage 5.0 6.958 1 22
Osa09LNT0434500.1 osa-miR1863c Cleavage 4.5 10.17 1 24
Osa09LNT0434500.1 osa-miR812n-3p Translation 5.0 15.564 1 24
Osa09LNT0434500.1 osa-miR5503 Cleavage 5.0 18.588 1 22
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa09LNT0434500.1 9 clr9 Resistance or Tolerance Cold tolerance RM285 RM434
Osa09LNT0434500.1 9 qPC9 Physiological trait Eating quality RM4413 RM1896
Osa09LNT0434500.1 9 qAC9 Physiological trait Eating quality RM4413 RM5122
Osa09LNT0434500.1 9 apd9 Others Others CDO590 G103
Osa09LNT0434500.1 9 nan Morphological trait Root C711 G103
Osa09LNT0434500.1 9 nan Resistance or Tolerance Drought tolerance R1164 R79
Osa09LNT0434500.1 9 nan Morphological trait Shoot/Seedling RG553 RZ206
pre-miRNA
Transcript ID Pre-miRNA Identity(%) Alignment Length Pre-miRNA start Pre-miRNA end E-value Bitscore
GWAS
Transcript ID Chromosome Locus Trait Value Plus Minus